Biosystems最新文献_第7页

The question of quantum communication between cancer cells 癌细胞之间的量子通讯问题

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-11 DOI: 10.1016/j.biosystems.2025.105562

Alberto Boretti

{"title":"The question of quantum communication between cancer cells","authors":"Alberto Boretti","doi":"10.1016/j.biosystems.2025.105562","DOIUrl":"10.1016/j.biosystems.2025.105562","url":null,"abstract":"<div><div>This letter evaluates the speculative hypothesis of quantum communication between cancer cells, contrasting it with well-established classical signaling mechanisms (e.g., chemical diffusion). While quantum physics permits entanglement-based information transfer, no direct empirical evidence supports this in biology. The focus is on biophotons (UPE) as potential mediators, citing Fritz-Albert Popp's coherence hypothesis. Proponents highlight delayed luminescence and non-classical photon statistics, while critics attribute UPE to random chemiluminescence and argue against sustained quantum coherence in noisy cellular environments. Other quantum signatures such as Fano resonances and vibronic coupling are also discussed. This paper advances a specific hypothesis that the unique metabolic and redox state of cancer cells could create conditions for transient, short-range quantum signaling mediated by biophotons. Though quantum effects like proton tunneling occur in cancer mutagenesis and enzymatic catalysis, these differ fundamentally from unproven intercellular quantum signaling. Photosynthesis' quantum coherence offers intriguing parallels, but cancer progression is well-explained classically. The hypothesis remains intriguing yet highly speculative, lacking robust empirical validation and facing significant theoretical hurdles related to decoherence and the maintenance of fragile quantum states. Rigorous experimental evidence is needed before accepting quantum mechanisms in cellular communication. This debate aligns with the burgeoning fields of bio photonics and quantum biology, urging interdisciplinary research to test these theoretical possibilities with advanced experimental techniques. Specific, testable protocols involving photon correlation measurements are proposed to validate or falsify this hypothesis.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105562"},"PeriodicalIF":1.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144842986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An Information Framework of Intelligence 情报的信息框架。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-09 DOI: 10.1016/j.biosystems.2025.105548

Michael E. Hochberg

{"title":"An Information Framework of Intelligence","authors":"Michael E. Hochberg","doi":"10.1016/j.biosystems.2025.105548","DOIUrl":"10.1016/j.biosystems.2025.105548","url":null,"abstract":"<div><div>Intelligence is a human construct to represent the ability to achieve goals. Given this wide berth, intelligence has been defined countless times, studied in a variety of ways and represented using numerous indicators. Understanding intelligence ultimately requires theory and quantification, both of which have proved elusive. I present an Information Framework of Intelligence (IFI) that applies across all systems from physics to biology, humans and AI. Central to this framework is the “intelligence niche”, which provides a conceptual basis for understanding constraints on intelligence and the evolution of intelligence. IFI likens intelligence to a real-time calculus, differentiating, correlating and integrating information, and anticipating or predicting future contingencies. I propose a classification of the levels and scales at which intelligence operates. Focussing on measurable macrosopic phenomena, I develop quantitative indicators of intelligence based on abilities to identify and resolve subgoals. Intelligence is reflected by acquired goal-useful information relative to goal complexity, or to the related concept of goal difficulty, or to an arbitrary reference such as a benchmark. I conclude with predictions and implications of IFI.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105548"},"PeriodicalIF":1.9,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144823096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Simulation peptide toxicity using the fragments of local symmetry in amino acid sequences 利用氨基酸序列局部对称片段模拟肽毒性

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-08 DOI: 10.1016/j.biosystems.2025.105554

Andrey A. Toropov , Alla P. Toropova , Valentin O. Kudyshkin , Emilio Benfenati , Danuta Leszczynska , Jerzy Leszczynski

引用次数: 0

The Metacontinuum: Bridging cellular composition to cognitive functions in brain organization 元连续体：连接细胞组成与大脑组织的认知功能

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-06 DOI: 10.1016/j.biosystems.2025.105550

Gustavo Guzmán, Elsa Magaña-Cuevas, Rocío Hernández-Rizo, Malinalli López-Medina, Omar Cano-Garcia, Omar Paredes

{"title":"The Metacontinuum: Bridging cellular composition to cognitive functions in brain organization","authors":"Gustavo Guzmán, Elsa Magaña-Cuevas, Rocío Hernández-Rizo, Malinalli López-Medina, Omar Cano-Garcia, Omar Paredes","doi":"10.1016/j.biosystems.2025.105550","DOIUrl":"10.1016/j.biosystems.2025.105550","url":null,"abstract":"<div><div>Brain organization emerges from molecular, cellular, and systems-level processes that together generate cognitive function. While individual biological codes have been characterized at specific scales, their integration across levels remains poorly understood. Existing theories of consciousness recognize diverse electrophysiological signatures but fail to explain the continuity linking molecular and neural codes. We propose the metacontinuum hypothesis as a unifying framework that connects these layers of biological information processing. Molecular codes establish cellular identity and circuit properties, while neural codes organize these circuits into systems supporting cognition. Evidence from connectomics, transcriptomics, and neuroimaging reveals mechanistic links between these levels, including gene expression gradients aligned with functional connectivity patterns. These findings suggest molecular and neural codes are coupled through bidirectional regulatory mechanisms. The metacontinuum hypothesis offers a roadmap for understanding biological information flow—from molecular interactions to neural computations—addressing the fragmentation problem in Code Biology and supporting the development of an integrated, multi-scale theory of life's coding architecture.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105550"},"PeriodicalIF":1.9,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144780852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

From reaction to reflection: A recursive framework for the evolution and structure of intelligence 从反应到反思：智能进化和结构的递归框架。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-05 DOI: 10.1016/j.biosystems.2025.105549

Joseph J. Trukovich

{"title":"From reaction to reflection: A recursive framework for the evolution and structure of intelligence","authors":"Joseph J. Trukovich","doi":"10.1016/j.biosystems.2025.105549","DOIUrl":"10.1016/j.biosystems.2025.105549","url":null,"abstract":"<div><div>Understanding emerges not from isolated cognitive abilities but from recursive depth—the capacity for self-referential processing grounded in systems with authentic thermodynamic constraints. The Reaction to Reflection (R2R) model advances a unifying principle for intelligence, identifying four evolutionary transitions in recursive sophistication: reaction (chemical recursion), temporogenesis (anticipatory prediction), symbiogenesis (cooperative integration), and cognogenesis (explicit self-referential modeling). We show that the transition from implicit recursion, in which systems engage recursive processes without representing them, to explicit recursion, in which recursion becomes a manipulable cognitive construct, accounts for the emergence of consciousness and the persistent gap between biological and artificial intelligence. Evidence from microbial decision-making, cross-kingdom signaling, and neural predictive and self-referential networks supports this framework. R2R generates testable predictions on cognitive dimensionality, provides criteria for assessing artificial consciousness, and reframes neurodevelopmental variation as alternative recursive architectures. By making biological grounding a precondition for genuine intelligence, R2R links objective neural dynamics to subjective experience within a unified mechanistic account.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105549"},"PeriodicalIF":1.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144776811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Brain and behavior share features of a critical state dynamics 大脑和行为具有临界状态动力学的共同特征。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-05 DOI: 10.1016/j.biosystems.2025.105551

Chetan K. Yadav , Yoganarasimha Doreswamy

引用次数: 0

The development of code systems during eukaryogenesis and the rise of multicellularity 真核发生过程中密码系统的发展和多细胞生物的兴起

IF 1.9 4区生物学

Biosystems Pub Date : 2025-07-31 DOI: 10.1016/j.biosystems.2025.105546

Abir U. Igamberdiev

{"title":"The development of code systems during eukaryogenesis and the rise of multicellularity","authors":"Abir U. Igamberdiev","doi":"10.1016/j.biosystems.2025.105546","DOIUrl":"10.1016/j.biosystems.2025.105546","url":null,"abstract":"<div><div>The expansion of the set of biological codes associated with the appearance and complexification of eukaryotic cells (eukaryogenesis) and the evolution of multicellularity is based on the development of higher codes operating over the genetic system. In the course of evolution, the perception-action functional cycles described by Jakob von Uexküll become complemented by the secondary meta-cycles, which perceive the work of the primary cycles, and finally by tertiary cycles of meta-reflexivity, which perceive and evaluate the previous activity of the secondary functional cycles and generate a new field of meanings associated with conscious experience. The development of secondary and tertiary cycles forms the basis of higher-level codes operating over the genetic system and resulting in the evolutionary separation between unikonts and bikonts, in the divergence between protostomes and deuterostomes, in all events of cellular differentiation manifested as differentiation trees, and finally in the appearance of consciousness. The expansion of codes associated with the rise of eukaryotic organelles and with the cytoskeleton rearrangements in the ontogenesis of multicellular organisms determines the course of the evolutionary process toward complexification. The internally controlled recombination process, in particular, in the course of meiotic cell division and ontogenetic differentiation, becomes the driving factor of progressive evolution. It corresponds to the growing role of the epigenome and epigenetic regulation in the complexification of biological organization. It is concluded that the evolutionary process unfolds as a propagating non-deducible construction following the generation of functional redundancy, which is achieved through gene duplication, symbiosis, and cell-cell interactions, and becomes an important precondition for the appearance of new evolutionary acquisitions.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105546"},"PeriodicalIF":1.9,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144758034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Uncovering dual oscillatory regimes in p53-mdm2 dynamics: A data-driven modeling approach with implications for cancer suppression 揭示p53-mdm2动力学中的双振荡机制：一种数据驱动的建模方法，具有癌症进展的意义。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-07-29 DOI: 10.1016/j.biosystems.2025.105540

Kathryn K. Menta , Majid Bani-Yaghoub , Bi-Botti C. Youan

{"title":"Uncovering dual oscillatory regimes in p53-mdm2 dynamics: A data-driven modeling approach with implications for cancer suppression","authors":"Kathryn K. Menta , Majid Bani-Yaghoub , Bi-Botti C. Youan","doi":"10.1016/j.biosystems.2025.105540","DOIUrl":"10.1016/j.biosystems.2025.105540","url":null,"abstract":"<div><div>Quantifying the dynamic interplay between p53 and Mdm2 is critical for uncovering their roles in cancer suppression and therapeutic targeting. Experimental studies have shown that p53-Mdm2 interactions exhibit oscillatory behavior in response to DNA damage. However, several mathematical models fail to sustain these oscillations or do not fit well with the experimental data, instead converging to constant steady-state values of p53 and Mdm2, which is unrealistic. In this study, we develop a simple yet robust ordinary differential equation model that accurately quantifies different stable periodic solutions (limit cycles) for p53-Mdm2 dynamics. Specifically, using a two-step numerical calibration algorithm, we validate the model against four experimental datasets. The calibrated model fits the data well and reveals two distinct oscillatory regimes: one in which Mdm2 oscillates with an amplitude 2.67 times greater than that of p53, suggesting a strongly amplified feedback response, and another in which Mdm2 exhibits variable but consistently lower-amplitude oscillations relative to p53. The observed variability in oscillatory behavior may support tumor suppression by enabling context-dependent activation of p53 targets, allowing cells to fine-tune stress responses.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105540"},"PeriodicalIF":1.9,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coupling of the energetic and purinergic activities of ATP in ischemic and hypoxic disease states 缺血和缺氧疾病状态下ATP的能量和嘌呤能活性的耦合。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-07-23 DOI: 10.1016/j.biosystems.2025.105544

William D. Ehringer, Kristyn H. Smith

{"title":"Coupling of the energetic and purinergic activities of ATP in ischemic and hypoxic disease states","authors":"William D. Ehringer, Kristyn H. Smith","doi":"10.1016/j.biosystems.2025.105544","DOIUrl":"10.1016/j.biosystems.2025.105544","url":null,"abstract":"<div><div>Adenosine-5′-triphosphate (ATP) is the single most important molecule in life. It is the universal energy currency of all living things. The energy from ATP is used in the synthesis of RNA/DNA, proteins, and lipids. The energy is used in signal transduction, ion pumping, intracellular and extracellular movement, and heat production. To meet the metabolic demand for ATP, cells utilize oxygen to extract maximal energy from substrates. The dependence on oxygen over the course of evolution allowed cells to grow in size and complexity, but at the same time cells became dependent upon oxygen for cell function and survival. During periods of ischemia or hypoxia, ATP produced by oxidative phosphorylation decreases, cells compensate by increasing glycolytic and substrate level phosphorylation, as well as prioritizing ATP consuming processes. If ischemia or hypoxia continues, extracellular ATP levels increase due to leakage and cell death, and ATP becomes an endogenous ligand that activates purinergic receptors located on cells throughout the body. ATP induces a purinergic response that can vary from cell death to cell proliferation, depending on the concentration of extracellular ATP. The coupling of the energetic and purinergic roles of ATP in ischemia or hypoxia is well illustrated in the leading causes of death in humans in the United States. Intracellular ATP depletion leads to cellular dysfunction and extracellular ATP leads to purinergic mediated responses that attempt to rectify the ischemia or hypoxia issue. Understanding the connections between the energetic and purinergic roles of ATP could be useful in future therapies.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"255 ","pages":"Article 105544"},"PeriodicalIF":1.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Two coherent definitions of the life process derived from the half-chaos theory and the (unintentional) purposeful information theory 半混沌理论和（无意的）目的信息论对生命过程的两个连贯定义。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-07-21 DOI: 10.1016/j.biosystems.2025.105533

Andrzej Gecow

{"title":"Two coherent definitions of the life process derived from the half-chaos theory and the (unintentional) purposeful information theory","authors":"Andrzej Gecow","doi":"10.1016/j.biosystems.2025.105533","DOIUrl":"10.1016/j.biosystems.2025.105533","url":null,"abstract":"<div><div>Most attempts to define life to date have consisted in indicating several features that, according to the author of the definition, occur in all cases that he considers life. Such an analytical path should have existed at the beginning. To this day, we do not have a \"good\" definition from which as many observed features of life result as possible. The derivation of specific features from the definition and additional assumptions is the structure of a deductive theory, which primarily explains and allows for understanding. The initial proposal for the framework of such a theory is presented in the book \"Draft of the Deductive Theory of Life\". There two coherent definitions of life are derived from ordered foundations - the half-chaos theory and unintentional purposeful information theory built for this task. These definitions can be classified as Darwinian. Both of these theories offer new perspectives on the issues described, and are briefly described in the article. Without these theories, the formulations of the given definitions are incomprehensible. Also, without deeper arguments that can be found in the book, the scope of the derived features of the life process and their place in the structure of the proposed theory is shown.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105533"},"PeriodicalIF":1.9,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0